A function called within `QL.fit`

to compute Poisson deviances of each gene for given design matrix

1 2 |

`counts` |
RNA-seq data matrix of integer expression counts. Each row contains observations from a single gene. Each column contains observations from a single experimental unit. |

`design` |
A single element from the |

`log.offset` |
A vector of log-scale, additive factors used to adjust estimated log-scale means for differences in library sizes across samples. Commonly used offsets include, |

`print.progress` |
logical. If TRUE, the function will provide an update on what gene number is being analyzed. Updates occur frequently to start then eventually occur every 5000 genes. Note that updates will not occur for one-factor designs, for which closed form solutions are available. |

list containing:

`dev` |
vector containing the deviance for each gene under a Poisson model fit to design matrix (or vector, for one-factor experiments) specified by |

`means` |
matrix of fitted mean values for each gene |

`parms` |
matrix of estimated coefficients for each gene |

Steve Lund lundsp@gmail.com

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.